Dear Freesurfer group,
When looking through the log after running recon-all, i have noticed two different errors in the logs. The one being about 'volumes differ in acquisition parameters' and the other 'Image geometries differ across time, maybe due to aquisition changes?'.
*Volumes differ in acquisition parametersv1acq fa=0.000000 tr=10.032000 te=0.000000 ti=0.000000v2acq fa=0.000000 tr=10.012000 te=0.000000 ti=0.000000WARNING: Image geometries differ across time, maybe due to aquisition changes?This can potentially bias a longitudinal study! Will continue in 10s.*
What do the above errors mean and is it something we should be worried about?
Best regards, Kasper Jessen MD, PhD Student
Hi Kasper
what was your input volume? The .02sec change in TR won't mean anything, although it is a bit surprising to see, as is the fact that the other parameters (flip angle, TE, etc...) don't seem to be preserved. We usually read those right out of the dicom files if that is what you used as input. Not sure why we would preserve the TR but not the other parameters.
cheers Bruce
On Sat, 10 Oct 2015, Kasper Jessen wrote:
Dear Freesurfer group,
When looking through the log after running recon-all, i have noticed two different errors in the logs. The one being about 'volumes differ in acquisition parameters' and the other 'Image geometries differ across time, maybe due to aquisition changes?'.
Volumes differ in acquisition parameters v1acq fa=0.000000 tr=10.032000 te=0.000000 ti=0.000000 v2acq fa=0.000000 tr=10.012000 te=0.000000 ti=0.000000 WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s.
What do the above errors mean and is it something we should be worried about?
Best regards, Kasper Jessen MD, PhD Student
Hi Bruce,
Thank you for your reply.
Initially a PAR/REC file was used to obtain an anat.nii file. This is used to create the [CROSS]. Two timepoints ([CROSS-1] and [CROSS-2]) was used to create the [BASE].
- Is it because there is too many file formats, and if so, how should this be managed? Is it possible to run freesurfer directly from the PAR/REC file? - Is the “Image geometries differ across time” related to the difference in acquisition parameters mentioned in the warning?
Best regards Kasper Jessen
2015-10-10 16:12 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Kasper
what was your input volume? The .02sec change in TR won't mean anything, although it is a bit surprising to see, as is the fact that the other parameters (flip angle, TE, etc...) don't seem to be preserved. We usually read those right out of the dicom files if that is what you used as input. Not sure why we would preserve the TR but not the other parameters.
cheers Bruce
On Sat, 10 Oct 2015, Kasper Jessen wrote:
Dear Freesurfer group,
When looking through the log after running recon-all, i have noticed two different errors in the logs. The one being about 'volumes differ in acquisition parameters' and the other 'Image geometries differ across
time,
maybe due to aquisition changes?'.
Volumes differ in acquisition parameters v1acq fa=0.000000 tr=10.032000 te=0.000000 ti=0.000000 v2acq fa=0.000000 tr=10.012000 te=0.000000 ti=0.000000 WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s.
What do the above errors mean and is it something we should be worried about?
Best regards, Kasper Jessen MD, PhD Student
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Kasper,
if you use the same file formats and conversion tools across both time points, the images should be identical. Even after conversion to nii. Not sure why they are not.
Yes, both warnings are related to the acquisition parameters. The second should better say that header information is different or something like that. I see if I can improve that error message to be more specific in a future release.
Best, Martin
On 10/17/2015 08:59 AM, Kasper Jessen wrote:
Hi Bruce,
Thank you for your reply.
Initially a PAR/REC file was used to obtain an anat.nii file. This is used to create the [CROSS]. Two timepoints ([CROSS-1] and [CROSS-2]) was used to create the [BASE].
- Is it because there is too many file formats, and if so, how should this be managed? Is it possible to run freesurfer directly from the PAR/REC file?
- Is the “Image geometries differ across time” related to the difference in acquisition parameters mentioned in the warning?
Best regards Kasper Jessen
2015-10-10 16:12 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:
Hi Kasper what was your input volume? The .02sec change in TR won't mean anything, although it is a bit surprising to see, as is the fact that the other parameters (flip angle, TE, etc...) don't seem to be preserved. We usually read those right out of the dicom files if that is what you used as input. Not sure why we would preserve the TR but not the other parameters. cheers Bruce On Sat, 10 Oct 2015, Kasper Jessen wrote: > > Dear Freesurfer group, > > When looking through the log after running recon-all, i have noticed two > different errors in the logs. The one being about 'volumes differ in > acquisition parameters' and the other 'Image geometries differ across time, > maybe due to aquisition changes?'. > > Volumes differ in acquisition parameters > v1acq fa=0.000000 tr=10.032000 te=0.000000 ti=0.000000 > v2acq fa=0.000000 tr=10.012000 te=0.000000 ti=0.000000 > WARNING: Image geometries differ across time, maybe due to aquisition > changes? > This can potentially bias a longitudinal study! Will continue in 10s. > > What do the above errors mean and is it something we should be worried > about? > > Best regards, > Kasper Jessen > MD, PhD Student > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.-- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j@cnsr.dk mailto:kasper_j@cnsr.dk eller kasper.jessen@regionh.dk mailto:kasper.jessen@regionh.dk
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Martin and FS experts.I am having difficulty in loading my qdec.table.dat to Matlab.When I use the [command: Qdec = fReadQdec('qdec.table.dat'); ] Matlab only recognises a matrix of 140x1 cell, whereas instead it should recognise a 140x4.I tried to import the table as 'table' from the gui interface but then I am getting error on the command: M = Qdec2num(Qdec,1) Any tips on how to load my table would be fabulous help.Thank youPabloTo: freesurfer@nmr.mgh.harvard.edu From: mreuter@nmr.mgh.harvard.edu Date: Mon, 19 Oct 2015 09:04:41 -0400 Subject: Re: [Freesurfer] Volumes differ in acquisition paramaters
Hi Kasper,
if you use the same file formats and conversion tools across both time points, the images should be identical. Even after conversion to nii. Not sure why they are not.
Yes, both warnings are related to the acquisition parameters. The second should better say that header information is different or something like that. I see if I can improve that error message to be more specific in a future release.
Best, Martin
On 10/17/2015 08:59 AM, Kasper Jessen wrote:
Hi Bruce,
Thank you for your reply.
Initially a PAR/REC file was used to obtain an anat.nii file. This is used to create the [CROSS]. Two timepoints ([CROSS-1] and [CROSS-2]) was used to create the [BASE].
Is it because there is too many file formats, and if so, how should this be managed? Is it possible to run freesurfer directly from the PAR/REC file?
Is the “Image geometries differ across time” related to the difference in acquisition parameters mentioned in the warning?
Best regards Kasper Jessen
2015-10-10 16:12 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Kasper
what was your input volume? The .02sec change in TR won't mean anything,
although it is a bit surprising to see, as is the fact that the other
parameters (flip angle, TE, etc...) don't seem to be preserved. We usually
read those right out of the dicom files if that is what you used as input.
Not sure why we would preserve the TR but not the other parameters.
cheers
Bruce
On Sat, 10 Oct 2015, Kasper Jessen wrote:
>
> Dear Freesurfer group,
>
> When looking through the log after running recon-all, i have noticed two
> different errors in the logs. The one being about 'volumes differ in
> acquisition parameters' and the other 'Image geometries differ across time,
> maybe due to aquisition changes?'.
>
> Volumes differ in acquisition parameters
> v1acq fa=0.000000 tr=10.032000 te=0.000000 ti=0.000000
> v2acq fa=0.000000 tr=10.012000 te=0.000000 ti=0.000000
> WARNING: Image geometries differ across time, maybe due to aquisition
> changes?
> This can potentially bias a longitudinal study! Will continue in 10s.
>
> What do the above errors mean and is it something we should be worried
> about?
>
> Best regards,
> Kasper Jessen
> MD, PhD Student
>
>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
--
Kasper Jessen, MD, PhD student
Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67
2600 Glostrup
Tlf.: 24430136
E-mail: kasper_j@cnsr.dk eller kasper.jessen@regionh.dk
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Pablo,
maybe your file is not clean and contains strange symbols to separate coumns and rows? Make sure columns are all separated by spaces. You could load the table into exel or openoffice spreadsheet and then export as CSV with space (or you could also try tab) for the separation and no "" around values.
Best, Martin
On 10/19/2015 11:32 AM, pablo najt wrote:
Dear Martin and FS experts. I am having difficulty in loading my qdec.table.dat to Matlab. When I use the [command:/Qdec = fReadQdec('qdec.table.dat');/ ] Matlab only recognises a matrix of 140x1 cell, whereas instead it should recognise a 140x4. I tried to import the table as 'table' from the gui interface but then I am getting error on the command: /M = Qdec2num(Qdec,1)/ Any tips on how to load my table would be fabulous help. Thank you Pablo
To: freesurfer@nmr.mgh.harvard.edu From: mreuter@nmr.mgh.harvard.edu Date: Mon, 19 Oct 2015 09:04:41 -0400 Subject: Re: [Freesurfer] Volumes differ in acquisition paramaters
Hi Kasper,
if you use the same file formats and conversion tools across both time points, the images should be identical. Even after conversion to nii. Not sure why they are not.
Yes, both warnings are related to the acquisition parameters. The second should better say that header information is different or something like that. I see if I can improve that error message to be more specific in a future release.
Best, Martin
On 10/17/2015 08:59 AM, Kasper Jessen wrote:
Hi Bruce, Thank you for your reply. Initially a PAR/REC file was used to obtain an anat.nii file. This is used to create the [CROSS]. Two timepoints ([CROSS-1] and [CROSS-2]) was used to create the [BASE]. * Is it because there is too many file formats, and if so, how should this be managed? Is it possible to run freesurfer directly from the PAR/REC file? * Is the “Image geometries differ across time” related to the difference in acquisition parameters mentioned in the warning? Best regards Kasper Jessen 2015-10-10 16:12 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi Kasper what was your input volume? The .02sec change in TR won't mean anything, although it is a bit surprising to see, as is the fact that the other parameters (flip angle, TE, etc...) don't seem to be preserved. We usually read those right out of the dicom files if that is what you used as input. Not sure why we would preserve the TR but not the other parameters. cheers Bruce On Sat, 10 Oct 2015, Kasper Jessen wrote: > > Dear Freesurfer group, > > When looking through the log after running recon-all, i have noticed two > different errors in the logs. The one being about 'volumes differ in > acquisition parameters' and the other 'Image geometries differ across time, > maybe due to aquisition changes?'. > > Volumes differ in acquisition parameters > v1acq fa=0.000000 tr=10.032000 te=0.000000 ti=0.000000 > v2acq fa=0.000000 tr=10.012000 te=0.000000 ti=0.000000 > WARNING: Image geometries differ across time, maybe due to aquisition > changes? > This can potentially bias a longitudinal study! Will continue in 10s. > > What do the above errors mean and is it something we should be worried > about? > > Best regards, > Kasper Jessen > MD, PhD Student > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j@cnsr.dk <mailto:kasper_j@cnsr.dk> eller kasper.jessen@regionh.dk <mailto:kasper.jessen@regionh.dk> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web :http://reuter.mit.edu
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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pablo najt